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Questions tagged [phylogenetics]

A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features.

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How to add taxa to a published tre file. What program to use? How to do it in Mesquite?

I need to add taxa to an already published tre file. (the Prum 2015 avian phylogeny). *For example if I wanted to add Western Gull to the tree (Larus occidentalis) knowing that Larus & Sterna are ...
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1answer
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How to define ammonites?

I miss the definition of ammonite. In my opinion, many authors confuse the term "Ammonite" and "Ammonoid". Ammonoids (Ammonoidea) are large group of cephalopods including for example goniatites (...
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How to create a phylogenetic tree (using Maximum Likelihood method) in newick format for a Multiple Sequence Alignment file in FASTA format?

The file size is really big (26.7 MB). So, I am unable to use the online web tools, as they cannot handle such large input data.
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327 views

What is the best argument for maximum parsimony method in phylogenetic tree construction?

Beside the fact that maximum parsimony is computationally cheap, what other good arguments are there for it? Is there any model behind this principle? Why would one expect this principle to provide ...
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Are phylogenetic tree construction algorithms any different than general clustering algorithms?

I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it ...
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Can anyone help me with these Biology evolutionary properties homework questions? [closed]

my teacher assigned these worksheet questions, they are ungraded, but he said something might come up on the test really similar to this so I really want to get all of them right. I am pretty ...
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How many times have Ecdysozoans made the transition to land? [duplicate]

In my evolutionary course we were taught that land plants are a monophyletic group, the transistion to land happened only once. The same goes for the tetrapods within the vertabrates. However this ...
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1answer
42 views

The phylogenetic definition of the clade Dinosauria

Up until two years ago the clade of Dinosauria was defined as all the descendants of the most recent common ancestor of Triceratops and birds. From Wikipedia: Under phylogenetic nomenclature, ...
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Question regarding when it's a homoplasy in a phylogenetic tree

If you have 2 organisms that both come directly from the same common ancestor on a phylogenetic tree, and that common ancestor does not have trait "x", is it possible for both of its direct ...
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Contructing phylogeny from an asymmetric distance matrix?

Is there any method for constructing a phylogenetic tree from a distance matrix which is not symmetric (i.e. the distance from A to be is not the same as the distance from B to A)? The distances I ...
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Were there any terrestrial species in the ancestry of all crustaceans?

To the exception of woodlice, Crustaceans live in aquatic (marine or freshwater) environments. Crustaceans are arthropods which is an immensely diverse taxon. Many arthropods live in terrestrial ...
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Is there a measure for degree of reticulation in a phylogenetic network?

When working with phylogenetic networks, how does one talk about reticulate (i.e., web-like) the branches are? Is there a standard measure of this?
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How to determine the number of parameters in a phylogenetic model?

I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?
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Have traditional categories such as phylum, class, genus, been dispensed with in modern taxonomy?

Looking through the one zoom and EOL projects I see no reference to such categories.
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Where can I find datasets containing large phylogenetic networks?

There are many datasets out there for phylogenetic trees, one can example can be found here. However, I couldn't find something for phylogenetic networks. According to Wikipedia: A phylogenetic ...
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1answer
246 views

The protostome/deuterostome distinction and why it is important

As I unerstand it, at some point an embryo develops a hole; this hole continues to punch through, and eventually makes an opening at the other side of the embryo. If the original hole becomes the ...
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1answer
111 views

Basic question about phylogenetic trees

The following is an illustration rom my book of the phylogenetic tree of 6 animal phyla (the red stuff is mine): I think what's causing some confusion is that there are no names/years at the circled ...
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What is the closest relative to odd-toed ungulate?

I have seen about 3 variation of phylogenetic tree about odd-toed ungulate and I don't know which one is really updated or outdated or which one have more backed up theory First is odd-toed ungulate ...
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2answers
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The parts of the phylogenetic nomenclature that need to be “unique”

I am not quite sure I have sorted through the diversity of approaches to nomenclature, but I had a specific question to help clarify what is going on. Basically I am just wondering what needs to be ...
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Example Clade Names in PhyloCode

After looking through the PhyloCode, the only thing I found that looked like an example was in Article 9, Chapter 4: A node-based definition may be abbreviated "<A&B" or "<A&B&C&...
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What could explain discrepancies between dates provided by the fossil record vs. the molecular clock?

I am studying a mud snail genus called Ecrobia. For the Caspian species (Ecrobia grimmi), there is a discrepancy between dates provided by the fossil record and the molecular clock: First appearance ...
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2answers
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Why the SNPs from the earliest human haplogroups are missing in people outside of Africa if they are infact the descendants of it?

The SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 from haplogroup A and SNPs M60, M181, P90 from haplogroup B are missing in people without recent African ...
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Estimating population divergence time with a single mitochondrial marker

Is it possible to estimate population divergence time with a single mitochondrial marker? Here is additional information for my specific case: Mitochondrial marker: Cytochrome Oxidase Subunit 1 (...
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1answer
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How would I represent this on a cladogram?

So, right now I am making a cladogram (More of a dendrogram) for a kingdom of fictional species, and I'm not exactly sure how to represent a certain relationship. Let's say that the oldest class in ...
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Are there any open phylogenetic projects that don't require coding to make a contribution

I am stay at home learner, not pursuing education formal education and currently doing a part time job. I've however completed masters in biotechnology and I'm studying to pursue PhD in molecular ...
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2answers
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MLE estimation with Mk model in ape or phangorn?

When doing MLE with the R package ape or phangorn, is it possible to set the substitution model to Mk? If so, how does one do this?
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1answer
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Minimum number of clades needed to partition Vertebrates while maintaining Birds, Mammals, and Amphibians as distinct clades?

At school I was taught the Linnaean view of vertebrate life - that vertebrate animals consisted of 5 distinct groups: mammals, birds, reptiles, amphibians, fish. I learned later however that this was ...
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How does one go from a couple of DNA sequences to a distance-matrix?

For a project we need to explain the subject of UPGMA. We think we understand thee method itself but I fail to see how you go from a number of DNA-sequences to the distance matrix. I understand ...
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1answer
46 views

Finding different Proteins with same function [closed]

Could you help me about finding two different proteins that coming from different ancestors, perform same function? Thank you
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4answers
2k views

If we sequenced the genome of every species, would all phylogenies agree?

The Tree of Life is still up for debate. Most of this debate seems to be due to a lack of genomic information, but that deficiency is decreasing rapidly with advances in technology and sequencing ...
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1answer
380 views

Forming a cladogram from a table of information

Can someone please give me some tips or help me build a cladogram from the following table of information? The outgroup is Lancelets and the first derived character is vertebrae, followed by Lampreys ...
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2answers
30 views

Is “Monophyly” context dependent?

I am thinking about this thought experiment: Suppose we have three taxa which are grouped into the following tree: {{A,B},C}, clearly {B,C} is a paraphyletic group. But if A go extinct in the near ...
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1answer
83 views

In what does Genetic clustering and Cline sharpness differ?

They are both ways to measure divergence in species but I'm not understanding in what exactly the differ if both use hybrid zones and gene frequencies in the study.
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how origin of koi carp is different from goldfish

where did koi-carp originate? how are they different from goldfish? Wikipedia say that goldfish originated by genetic mutation but what about koi-carps?
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Why outgroups are supposed to be ancestral?

I was reading about phylogenies and found many literatures said that outgroups contain the ancestrial trait, but why is that? Aren't they also experiencing the same amount of evolutionary time and (...
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2answers
610 views

When did birds and mammals diverge?

Which was the most recent common ancestor between mammals and birds? Form a rapid google research I could not find good answers. This site seems to imply it was at least 250 milions of years ago. ...
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369 views

Did insects and arachnids diverge before or after moving to land?

Question: Are arachnids and insects so distantly related that they were already diverging before their (independent) emergence(s) on land? I am curious to know what the fossil record and molecular ...
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1answer
99 views

How would homologous recombination and mutations affect speciation?

I'm wondering how homologous recombination and mutations can affect how speciation can occur from one species (so that 2 will be created). I'm doing research and I found that different mutations and ...
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2answers
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Question about phylogenies and DNA sequencing

I'm reading this web page which talks about phylogenies and DNA sequencing: https://bioinf.comav.upv.es/courses/biotech3/theory/phylogeny.html A certain sentence says, "If we consider dolphins and ...
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1answer
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Is it possible for parsimony to estimate more state changes than stochastic character mapping

I'm mapping states (geographic regions) onto a phylogeny to estimate the number of transmissions between countries. I'm using two methods, stochastic character mapping implemented in Phytools and ...
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1answer
103 views

Finding phylogenetic distance between sequences?

I'm working on a piece of software that does comparative genomic analysis; and I found out in homology methods for functional annotation, it's preferable to pick the high scoring homolog from a ...
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1answer
23 views

computing relative synonymous codon usage from a coding sequence alignment while accounting for phylogenetic inertia?

I would like to compute the relative synonymous codon usage (RSCU) from coding sequence alignments. But since the coding sequences from an alignment are not independent realization, the statistics (...
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1answer
104 views

More informative phylogenetic trees

In the presentation of phylogenetic trees, the geometric shape of the trees often seems somehow arbitrary and is more driven by aesthetics than by informative reasons. But wouldn't it make sense to ...
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1answer
115 views

Has the most recent common ancestor of all living birds lived after dinosaur mass extinction?

I wonder if one or more phylogenetic threads of dinosaurs survived the mass extinction. In other words, are all living birds equally related to any given ancient dinosaur, or do some birds relate ...
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2answers
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“50% of the variance in antisocial phenotypes is the result of genetic factors” means what?

How can i understand the following sentence: Overall, the conclusions reached by these studies have been highly consistent in showing that approximately 50% of the variance in antisocial phenotypes ...
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2answers
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Did Carl Linnaeus ever name a species he never saw?

According to this post Carl Linnaeus named more than 13,000 species which is definitely quite impressive. If we consider a 50 years career it makes about 5 species per week! It would feel impressive ...
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523 views

How to interpret weighted Robinson-Foulds distance between phylogenies?

The Robinson-Foulds (RF) metric provides symmetric distance between two phylogenies as a sum of monophyletic groups present in one tree but not in the other. The normalised RF distance is given as $\...
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2answers
93 views

Manipulating phylogenetic trees

I am looking to manipulate manually constructed phylogenetic trees (adding bootstrap values, markers to indicate trate loss/gain etc.) I came across a paper that used Macclade, however, this no longer ...
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2answers
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Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits?

My question is contextualised for basic phylogeny knowledge. Here is my understanding: similar or identical traits between any two species, at the basic level, can be either homologous, meaning the ...
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What is the difference between phylogroup and subclade? [closed]

Looking for clarification in terminology, examples would be greatly appreciated! Not sure how this is off-topic. It is a general question about the difference between biological concepts defined in ...